From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 16 Sep 2013 14:46:00 +0000 (+0000)
Subject: fixed overlap bug in patscan_seq
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=847dcea71d11154d6636abc7257d2ff1af83bcde

fixed overlap bug in patscan_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2197 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index f408bd6..a209bc6 100755
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -51,7 +51,7 @@ class Patscan
       args << "scan_for_matches"
       args << "-c"                         if options[:comp]
       args << "-p"                         if options[:seq_type] == :protein
-      args << "-o"                         if options[:overlap]
+      args << "-o 1"                       if options[:overlap]
       args << "-n #{options[:max_misses]}" if options[:max_misses]
       args << "-m #{options[:max_hits]}"   if options[:max_hits]
       args << File.join(@tmp_dir, "#{i}.pat")
diff --git a/bp_test/out/patscan_seq.out.4 b/bp_test/out/patscan_seq.out.4
index 42fb5f5..d3fd5fc 100644
--- a/bp_test/out/patscan_seq.out.4
+++ b/bp_test/out/patscan_seq.out.4
@@ -1,30 +1,70 @@
 KEY: VALUE
 ---
-SEQ_NAME: test1
-SEQ: LLRVDNIIRARPRTANRQHM
+SEQ_NAME: test
+SEQ: GGACTACNNGGGTATCTAATAGTC
 SEQ_LEN: 20
 ---
 REC_TYPE: PATSCAN
-S_ID: test1
-Q_ID: RARP
-MATCH: RARP
-S_BEG: 8
+S_ID: test
+Q_ID: GG
+MATCH: GG
+S_BEG: 0
+S_END: 1
+STRAND: +
+SCORE: 100
+MATCH_LEN: 2
+---
+REC_TYPE: PATSCAN
+S_ID: test
+Q_ID: GG
+MATCH: GG
+S_BEG: 9
+S_END: 10
+STRAND: +
+SCORE: 100
+MATCH_LEN: 2
+---
+REC_TYPE: PATSCAN
+S_ID: test
+Q_ID: GG
+MATCH: GG
+S_BEG: 10
 S_END: 11
 STRAND: +
 SCORE: 100
-MATCH_LEN: 4
+MATCH_LEN: 2
 ---
 SEQ_NAME: test2
-SEQ: NIIRARPRTAN
-SEQ_LEN: 11
+SEQ: GGACTACNNGGGTATCTAATGCATACG
+SEQ_LEN: 27
 ---
 REC_TYPE: PATSCAN
 S_ID: test2
-Q_ID: RARP
-MATCH: RARP
-S_BEG: 3
-S_END: 6
+Q_ID: GG
+MATCH: GG
+S_BEG: 0
+S_END: 1
+STRAND: +
+SCORE: 100
+MATCH_LEN: 2
+---
+REC_TYPE: PATSCAN
+S_ID: test2
+Q_ID: GG
+MATCH: GG
+S_BEG: 9
+S_END: 10
+STRAND: +
+SCORE: 100
+MATCH_LEN: 2
+---
+REC_TYPE: PATSCAN
+S_ID: test2
+Q_ID: GG
+MATCH: GG
+S_BEG: 10
+S_END: 11
 STRAND: +
 SCORE: 100
-MATCH_LEN: 4
+MATCH_LEN: 2
 ---
diff --git a/bp_test/out/patscan_seq.out.5 b/bp_test/out/patscan_seq.out.5
index bf37a96..42fb5f5 100644
--- a/bp_test/out/patscan_seq.out.5
+++ b/bp_test/out/patscan_seq.out.5
@@ -3,20 +3,28 @@ KEY: VALUE
 SEQ_NAME: test1
 SEQ: LLRVDNIIRARPRTANRQHM
 SEQ_LEN: 20
-PATTERN: RARP
+---
+REC_TYPE: PATSCAN
+S_ID: test1
+Q_ID: RARP
 MATCH: RARP
 S_BEG: 8
 S_END: 11
 STRAND: +
+SCORE: 100
 MATCH_LEN: 4
 ---
 SEQ_NAME: test2
 SEQ: NIIRARPRTAN
 SEQ_LEN: 11
-PATTERN: RARP
+---
+REC_TYPE: PATSCAN
+S_ID: test2
+Q_ID: RARP
 MATCH: RARP
 S_BEG: 3
 S_END: 6
 STRAND: +
+SCORE: 100
 MATCH_LEN: 4
 ---
diff --git a/bp_test/out/patscan_seq.out.6 b/bp_test/out/patscan_seq.out.6
new file mode 100644
index 0000000..bf37a96
--- /dev/null
+++ b/bp_test/out/patscan_seq.out.6
@@ -0,0 +1,22 @@
+KEY: VALUE
+---
+SEQ_NAME: test1
+SEQ: LLRVDNIIRARPRTANRQHM
+SEQ_LEN: 20
+PATTERN: RARP
+MATCH: RARP
+S_BEG: 8
+S_END: 11
+STRAND: +
+MATCH_LEN: 4
+---
+SEQ_NAME: test2
+SEQ: NIIRARPRTAN
+SEQ_LEN: 11
+PATTERN: RARP
+MATCH: RARP
+S_BEG: 3
+S_END: 6
+STRAND: +
+MATCH_LEN: 4
+---
diff --git a/bp_test/test/test_patscan_seq b/bp_test/test/test_patscan_seq
index abb1ac7..c00c96f 100755
--- a/bp_test/test/test_patscan_seq
+++ b/bp_test/test/test_patscan_seq
@@ -14,10 +14,14 @@ run "$bp -I $in.1 -p GACT -i -O $tmp"
 assert_no_diff $tmp $out.3
 clean
 
-run "$bp -I $in.2 -p RARP -O $tmp"
+run "$bp -I $in.1 -o -p GG -O $tmp"
 assert_no_diff $tmp $out.4
 clean
 
-run "$bp -I $in.2 -p RARP -i -O $tmp"
+run "$bp -I $in.2 -p RARP -O $tmp"
 assert_no_diff $tmp $out.5
 clean
+
+run "$bp -I $in.2 -p RARP -i -O $tmp"
+assert_no_diff $tmp $out.6
+clean